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For example, GRPS can be based on SNPs that are selected based on functional annotation or physical position in the genome. In this framework, genetic variance is estimated from genetic similarity among pairs of individuals who are not related in the classical sense. The basic idea behind this method is that for a polygenic trait, pairs of individuals who show higher genetic similarity also show higher resemblance at the trait level.
Genetic similarity for each pair of individuals (defined in the model as sharing 0, 1 or 2 alleles at each locus) is measured from all the SNPs and the aggregated SNP effects are treated as random variables in a mixed linear model (Yang et al.
The variance of y is the sum of the genetic variance, the interaction variance and the error variance.